Our paper presents an application case study of a recently published sediment transport calculation method. In the last few decades, important bed changes have taken place along a Danube section (rkm 1798 and rkm 1794), which caused primary problems, e.g., for navigation, flood risk management, and habitat-related processes. The earlier-presented studies highlighted the need for 3D CFD morphodynamic model investigation in order to estimate the expectable future changes. However, none of the sediment transport models in the literature are able to deal with the spatially and temporally varied dominant grain size in the bed load. For such a river section, a novel calculation method and its verification were presented in 2017, which is able to deal with such complexity. Therefore, the use of the novel method becomes justified. The model investigations result in important statements: the trendy bed level incision in the main channel is not expected anymore, but the formation of the new dynamic equilibrium state is presumable. Minor bed changes can take place in the groin fields and at the gravel bars in small time scale (e.g., during a flood wave), but no trendy erosion or sedimentation can be detected in the years scale.